SMTL ID : 1yq3.1

Avian respiratory complex ii with oxaloacetate and ubiquinone

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.1: 39 residues within 4Å: Chain A: V.24, G.25, A.26, G.27, G.28, A.29, V.47, T.48, K.49, L.50, S.55, H.56, T.57, A.59, A.60, Q.61, G.62, G.63, Y.176, F.177, A.178, A.212, T.213, G.214, T.224, D.232, L.263, H.364, Y.365, G.396, E.397, R.408, A.411, N.412, S.413, L.414, L.417 Chain B: E.67 Ligands: TEO.2 36 PLIP interactions: 36 interactions with chain A Hydrophobic interactions: A:A.59, A:L.263, A:L.263 Hydrogen bonds: A:A.26, A:A.26, A:G.28, A:A.29, A:T.48, A:K.49, A:K.49, A:L.50, A:L.50, A:S.55, A:H.56, A:T.57, A:T.57, A:Q.61, A:G.63, A:G.63, A:A.178, A:G.214, A:D.232, A:E.397, A:R.408, A:R.408, A:A.411, A:S.413, A:S.413, A:L.414 Water bridges: A:G.27, A:G.30, A:Y.365, A:E.397, A:E.397, A:A.398 pi-Cation interactions: A:H.364

1 x TEO: MALATE LIKE INTERMEDIATE(Non-covalent)

TEO.2: 13 residues within 4Å: Chain A: Q.61, G.62, F.130, H.253, L.263, T.265, E.266, R.297, H.364, R.408, G.410, A.411 Ligands: FAD.1 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.62, A:H.253, A:E.266, A:R.297, A:R.297, A:A.411 Salt bridges: A:H.253, A:R.297, A:R.297, A:H.364, A:R.408

30 x UNL: UNKNOWN LIGAND(Non-covalent)(Non-functional Binders)

UNL.3: 1 residues within 4Å: Chain A: E.540 Ligand excluded by PLIP UNL.4: 1 residues within 4Å: Chain A: R.511 Ligand excluded by PLIP UNL.5: 3 residues within 4Å: Chain A: R.167, Y.168, D.169 Ligand excluded by PLIP UNL.6: 3 residues within 4Å: Chain A: I.602, D.603, R.604 Ligand excluded by PLIP UNL.7: 1 residues within 4Å: Chain A: A.429 Ligand excluded by PLIP UNL.8: 1 residues within 4Å: Chain A: Q.331 Ligand excluded by PLIP UNL.9: 1 residues within 4Å: Chain A: S.440 Ligand excluded by PLIP UNL.10: 2 residues within 4Å: Chain A: D.73, L.135 Ligand excluded by PLIP UNL.11: 2 residues within 4Å: Chain A: D.73, W.78 Ligand excluded by PLIP UNL.12: 3 residues within 4Å: Chain A: V.290, S.620, Y.621 Ligand excluded by PLIP UNL.13: 2 residues within 4Å: Chain A: E.121 Chain B: I.146 Ligand excluded by PLIP UNL.14: 2 residues within 4Å: Chain A: T.475, K.495 Ligand excluded by PLIP UNL.15: 3 residues within 4Å: Chain A: R.309, E.310, G.311 Ligand excluded by PLIP UNL.16: 1 residues within 4Å: Chain A: E.608 Ligand excluded by PLIP UNL.17: 1 residues within 4Å: Chain A: P.329 Ligand excluded by PLIP UNL.22: 2 residues within 4Å: Chain B: R.10, P.91 Ligand excluded by PLIP UNL.23: 3 residues within 4Å: Chain B: K.123 Chain C: T.3, A.5 Ligand excluded by PLIP UNL.24: 1 residues within 4Å: Chain B: Y.245 Ligand excluded by PLIP UNL.25: 3 residues within 4Å: Chain B: H.104, W.173 Ligands: UNL.33 Ligand excluded by PLIP UNL.26: 1 residues within 4Å: Chain B: F.210 Ligand excluded by PLIP UNL.27: 3 residues within 4Å: Chain B: D.208, P.209 Chain D: A.6 Ligand excluded by PLIP UNL.32: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.33: 3 residues within 4Å: Chain C: L.23, H.26 Ligands: UNL.25 Ligand excluded by PLIP UNL.34: 1 residues within 4Å: Chain C: I.29 Ligand excluded by PLIP UNL.35: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.37: 1 residues within 4Å: Chain D: L.19 Ligand excluded by PLIP UNL.38: 2 residues within 4Å: Chain D: P.33, A.34 Ligand excluded by PLIP UNL.39: 1 residues within 4Å: Chain D: H.9 Ligand excluded by PLIP UNL.40: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.41: 2 residues within 4Å: Chain D: Y.30, P.31 Ligand excluded by PLIP

1 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.18: 11 residues within 4Å: Chain B: S.64, C.65, R.66, G.68, I.69, C.70, G.71, S.72, C.73, L.83, C.85 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.65, B:C.70, B:C.73, B:C.85

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.19: 13 residues within 4Å: Chain B: C.158, I.159, L.160, C.161, A.162, C.163, C.164, A.182, M.185, C.225, P.226, K.227, P.231 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.158, B:C.161, B:C.164, B:C.225

1 x F3S: FE3-S4 CLUSTER(Non-covalent)

F3S.20: 12 residues within 4Å: Chain B: C.168, Y.178, P.181, C.215, H.216, T.217, I.218, M.219, N.220, C.221, G.232, I.235 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.168, B:C.215, B:C.221

1 x UQ: Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer(Non-covalent)

UQ.21: 10 residues within 4Å: Chain B: P.169, W.173, I.218 Chain C: I.27, W.32, M.36, S.39, I.40, R.43 Chain D: Y.58 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:I.27, C:W.32, B:P.169, B:W.173 Hydrogen bonds: C:I.40 Water bridges: C:R.43, C:R.43

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.28: 3 residues within 4Å: Chain B: I.11, K.13, L.93 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.93

1 x JZR: hexyl beta-D-glucopyranoside(Non-covalent)

JZR.29: 7 residues within 4Å: Chain B: R.223 Chain C: K.31, W.32, S.33, L.34, P.35, E.120 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:W.32, C:W.32 Hydrogen bonds: C:K.31, C:K.31, C:L.34, C:E.120, B:R.223

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.30: 20 residues within 4Å: Chain B: H.216 Chain C: H.42, R.43, G.46, V.47, L.49, S.50, H.98, T.99, G.102, H.105 Chain D: R.14, S.17, L.20, L.21, L.24, L.43, H.46, G.50, L.51 22 PLIP interactions: 7 interactions with chain D, 12 interactions with chain C, 3 interactions with chain B, Hydrophobic interactions: D:L.20, D:L.24, D:L.43, D:L.51, C:L.49, C:L.49, C:T.99, C:H.105 Hydrogen bonds: D:R.14, D:G.50 Metal complexes: D:H.46, C:H.98 Water bridges: C:H.42, C:H.42, C:R.43, C:H.105, C:H.105, B:H.216, B:T.217 Salt bridges: C:R.43, C:H.105, B:H.216

2 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)

PEE.31: 7 residues within 4Å: Chain C: L.95, S.96, W.100 Chain D: A.18, G.22, L.24 Ligands: PEE.36 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.95, C:W.100, D:L.24 Hydrogen bonds: D:G.22 PEE.36: 8 residues within 4Å: Chain C: V.92, I.137 Chain D: L.24, A.27, Y.28, V.97, W.101 Ligands: PEE.31 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:L.24, D:A.27, D:V.97, D:W.101, D:W.101, D:W.101, D:W.101, C:V.92, C:I.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, L. et al., 3-Nitropropionic Acid Is a Suicide Inhibitor of Mitochondrial Respiration That, upon Oxidation by Complex II, Forms a Covalent Adduct with a Catalytic Base Arginine in the Active Site of the Enzyme. J.Biol.Chem. (2006)

Release Date

2005-12-20

Peptides

Succinate dehydrogenase flavoprotein subunit: A
succinate dehydrogenase Ip subunit: B
SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNIT: C
SUCCINATE DEHYDROGENASE CYTOCHROME B, SMALL SUBUNIT: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Succinate dehydrogenase flavoprotein subunit

succinate dehydrogenase Ip subunit

SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNIT

SUCCINATE DEHYDROGENASE CYTOCHROME B, SMALL SUBUNIT

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